Tools   Select Another Resource Report Type

https://www.openclinica.com/

Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.

Proper citation: OpenClinica (RRID:SCR_019223) Copy   

•   Source: SciCrunch Registry

http://www.neuro.uni-jena.de/cat/

Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.

Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=tidyverse

Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.

Proper citation: tidyverse (RRID:SCR_019186) Copy   

•   Source: SciCrunch Registry

https://sils.fnwi.uva.nl/bcb/objectj/

Software tool used for non destructive marking and linked results in ImageJ. Integrates image analysis across many images or stacks into single project file.

Proper citation: ObjectJ (RRID:SCR_019190) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=NBR

Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.

Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy   

•   Source: SciCrunch Registry

https://long-read-tools.org/

Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies.

Proper citation: long-read-tools (RRID:SCR_019116) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/pdbe/emdb/empiar/

Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers.

Proper citation: Electron Microscopy Public Image Archive (RRID:SCR_019237) Copy   

•   Source: SciCrunch Registry

https://run.biosimulations.org

Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.

Proper citation: runBioSimulations (RRID:SCR_019110) Copy   

•   Source: SciCrunch Registry

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019231.pdf

HoloMonitor live cell imaging and analysis system by Phase Holographic Imaging PHI AB. Contains small, digital live cell, quantitative phase imaging microscope HoloMonitor M4 designed to operate constantly inside incubator and HoloMonitor cell imaging software App Suite or Hstudio to continuously monitor and quantitatively analyze both individual cells and cell populations over time without any cellular labels or stains. Microscope can operate in cell incubator, hypoxia chamber or on lab bench.

Proper citation: Phase Holographic Imaging: HoloMonitor live cell imaging and analysis system (RRID:SCR_019231) Copy   

•   Source: SciCrunch Registry

https://biosimulators.org

Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects.

Proper citation: BioSimulators (RRID:SCR_019111) Copy   

•   Source: SciCrunch Registry

https://jtremblay.github.io/amplicontagger.html

Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications.

Proper citation: AmpliconTagger (RRID:SCR_019112) Copy   

•   Source: SciCrunch Registry

https://www.elektralabs.com/solutions/education

Free curriculum, resources, and research for those considering incorporation of remote health monitoring.

Proper citation: Elektra Academy (RRID:SCR_019234) Copy   

•   Source: SciCrunch Registry

https://trials.bgcarlisle.com/

Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.

Proper citation: Clinical Trials Viewer (RRID:SCR_019230) Copy   

•   Source: SciCrunch Registry

http://www.phidot.org/software/mark/background/

Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals.

Proper citation: Program MARK (RRID:SCR_019281) Copy   

•   Source: SciCrunch Registry

https://github.com/bgcarlisle/Numbat

Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context.

Proper citation: Numbat (RRID:SCR_019207) Copy   

•   Source: SciCrunch Registry

https://galactic.biorelate.com

Platform of Biorelate to all auto curated data captured from millions of textual articles. Galactic lets you build intuitive queries and explore results through different views that best suit your research needs.Used by pharmaceutical and biotech companies to explore auto curated knowledge from millions of text sources, revealing hidden insights that might otherwise be lost.

Proper citation: Galactic (RRID:SCR_019208) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/variancePartition/

Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.

Proper citation: variancePartition (RRID:SCR_019204) Copy   

•   Source: SciCrunch Registry

https://www.brainlatam.com/knowledge-base/brainvision-pycorder-installation-262

Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data.

Proper citation: BrainVision PyCorder (RRID:SCR_019286) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=simr

Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.

Proper citation: SIMR (RRID:SCR_019287) Copy   

•   Source: SciCrunch Registry

http://metagenomics.iiserb.ac.in/mp3/

Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MP3 tool (RRID:SCR_019282) Copy   

•   Source: SciCrunch Registry